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protocols::minimization_packing::RotamerTrialsMover Class Reference

#include <RotamerTrialsMover.hh>

Inheritance diagram for protocols::minimization_packing::RotamerTrialsMover:
Inheritance graph
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Public Types

typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
typedef protocols::moves::MoverOP MoverOP
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 RotamerTrialsMover ()
 
 RotamerTrialsMover (ScoreFunctionCOP scorefxn_in, PackerTask &task_in)
 constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE More...
 
 RotamerTrialsMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in)
 constructor with TaskFactory More...
 
 RotamerTrialsMover (RotamerTrialsMover const &rval)
 copy constructor More...
 
 ~RotamerTrialsMover () override
 destructor More...
 
protocols::moves::MoverOP clone () const override
 clone this object More...
 
protocols::moves::MoverOP fresh_instance () const override
 create this type of object More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void score_function (core::scoring::ScoreFunctionCOP sf)
 
void task_factory (core::pack::task::TaskFactoryCOP tf)
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_rotamer_trials_mover (utility::tag::XMLSchemaDefinition &xsd)
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Protected Member Functions

ScoreFunctionCOP scorefxn () const
 read access for derived classes More...
 
PackerTaskCOP task (core::pose::Pose const &pose) const
 read access for derived classes, pose needed to run TaskFactory More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Private Attributes

ScoreFunctionCOP scorefxn_
 RotamerTrailsMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable. More...
 
PackerTaskOP task_
 use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply() More...
 
TaskFactoryCOP factory_
 TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable. More...
 
bool show_packer_task_
 showing contents of PackerTask ( default false ) More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover ( )
protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover ( ScoreFunctionCOP  scorefxn_in,
PackerTask task_in 
)

constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE

References core::pack::task::PackerTask::clone(), task_, and protocols::moves::Mover::type().

protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover ( ScoreFunctionCOP  scorefxn_in,
TaskFactoryCOP  factory_in 
)

constructor with TaskFactory

References protocols::moves::Mover::type().

protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover ( RotamerTrialsMover const &  rval)
default

copy constructor

protocols::minimization_packing::RotamerTrialsMover::~RotamerTrialsMover ( )
overridedefault

destructor

Member Function Documentation

void protocols::minimization_packing::RotamerTrialsMover::apply ( core::pose::Pose )
overridevirtual
RotamerTrialsMover::MoverOP protocols::minimization_packing::RotamerTrialsMover::clone ( ) const
overridevirtual
utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover ( utility::tag::XMLSchemaDefinition &  xsd)
static
RotamerTrialsMover::MoverOP protocols::minimization_packing::RotamerTrialsMover::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::minimization_packing::RotamerTrialsMover::get_name ( ) const
overridevirtual
std::string protocols::minimization_packing::RotamerTrialsMover::mover_name ( )
static
void protocols::minimization_packing::RotamerTrialsMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::minimization_packing::RotamerTrialsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::minimization_packing::RotamerTrialsMover::score_function ( core::scoring::ScoreFunctionCOP  sf)

References scorefxn_.

RotamerTrialsMover::ScoreFunctionCOP protocols::minimization_packing::RotamerTrialsMover::scorefxn ( ) const
protected

read access for derived classes

References scorefxn_.

Referenced by protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), and show().

void protocols::minimization_packing::RotamerTrialsMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References scorefxn().

Referenced by protocols::minimization_packing::operator<<().

RotamerTrialsMover::PackerTaskCOP protocols::minimization_packing::RotamerTrialsMover::task ( core::pose::Pose const &  pose) const
protected

read access for derived classes, pose needed to run TaskFactory

read access for derived classes

References factory_, and task_.

Referenced by apply(), and protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply().

void protocols::minimization_packing::RotamerTrialsMover::task_factory ( core::pack::task::TaskFactoryCOP  tf)

References factory_.

Referenced by parse_my_tag().

Member Data Documentation

TaskFactoryCOP protocols::minimization_packing::RotamerTrialsMover::factory_
private

TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable.

Referenced by task(), and task_factory().

ScoreFunctionCOP protocols::minimization_packing::RotamerTrialsMover::scorefxn_
private

RotamerTrailsMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable.

Referenced by apply(), parse_my_tag(), score_function(), and scorefxn().

bool protocols::minimization_packing::RotamerTrialsMover::show_packer_task_
private

showing contents of PackerTask ( default false )

Referenced by apply(), and parse_my_tag().

PackerTaskOP protocols::minimization_packing::RotamerTrialsMover::task_
private

use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply()

Referenced by RotamerTrialsMover(), and task().


The documentation for this class was generated from the following files: